Episode 82      24 min 46 sec
Breeding alpacas, starfish seeking refuge

PhD students Kate Naughton and Felicity Jackling discuss their respective research into ocean refuges and applying genetics to the commercial breeding of alpacas. With science host Shane Huntington.

"If you identify your source population and you can protect that source population well, then you’re doing a really good thing, not only for that ecosystem but for the surrounding ecosystems if they need to recover from damage" - Kate Naughton




           



Kate Naughton
Kate Naughton

Kate Naughton is currently doing a PhD in the Department of Genetics at the University of Melbourne. Kate's research focusses broadly on the past and present connectivity between populations of marine organisms of the southern Australian coast. She is specifically looking at shallow water echinoderm species (starfish, brittle stars, and crinoids). Her project is also supported and supervised by the Sciences Department at Museum Victoria.

Felcity Jackling
Felcity Jackling

Felicity Jackling is a PhD student in the Department of Genetics at the University of Melbourne. Felicity's research investigates the genetic basis of a number of congenital abnormalities in alpacas. The incidence of congenital disorders in alpacas is significantly higher than for other domesticated livestock and may be the result of a history of population bottlenecks in worldwide alpaca populations. The ultimate aim of this project is the development of genetic tests for these disorders that can be used to improve the national alpaca herd.

Credits

Host: Dr Shane Huntington
Producers: Kelvin Param, Eric van Bemmel, and Dr Shane Huntington
Series Creators: Eric van Bemmel and Kelvin Param
Audio Engineer: Russell Evans
Voiceover: Nerissa Hannink
Theme Music performed by Sergio Ercole. Mr Ercole is represented by the Musicians' Agency, Faculty of Music

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Starfish refugia and applied genetics in alpaca breeding

VOICEOVER
Welcome to Up Close, the research, opinion and analysis podcast from the University of Melbourne, Australia.  Up Close is available at upclose.unimelb.edu.au.

SHANE HUNTINGTON
Hello, and welcome to Up Close, coming to you from Melbourne University, Australia.  I’m Dr Shane Huntington.  Today on Up Close we look at two topics of interest being researched by University of Melbourne PhD students.  

First we are joined by Miss Kate Naughton, from the Department of Genetics at the University of Melbourne, Australia.  Kate is studying the temperate Australian marine environment, using genetics. Kate is testing the hypothesis that areas of high genetic diversity are actually glacial refuges, or refugia as some scientists call them, areas to which the range of species will contract when conditions are unfavourable.  Welcome to Up Close, Kate.

KATE NAUGHTON
Thank you.

SHANE HUNTINGTON
Now let’s talk about ecosystems first.  When you have these scenarios where there are significant climate shifts, say for example an ice age or the sorts of things we’re starting to experience at the moment, what happens to ecosystems?

KATE NAUGHTON
Well, it sort of happens - you have to sort of look at it from the building blocks of an ecosystem, which is on a species by species level.  Individual species have three fates: they can adapt, they can migrate, or they can basically go extinct.  That’s their option.  When you’re actually looking at an ecosystem level the situation gets a lot more complex.  Because, for example, say your prey species is one of the species to go extinct, then you’re in trouble.  Or if your predator goes extinct then you can expand as much as you like, or migrate or adapt or whatever.  So it’s a very complex situation when you’re looking at an ecosystem level.

SHANE HUNTINGTON
When we look at individual species, what is it that allows some of them to survive compared to some others dying out?  I mean you mentioned migration, but I assume there are other elements of breeding patterns, of how many offspring they have, all of these things must play into that in some way.

KATE NAUGHTON
Yeah, very much so.  Some species tend to be more adaptable to rapid change.  If, for example, you have a short generation, you reproduce quickly, and you produce many offspring, that often helps.  Leaving aside the question of what your competitors, predators and prey species are doing, there’s also the question of pre-existing genetic diversity to, say, how adaptable a population is.  For example, the more diverse a species is, usually the more room there is for adaptability.  And this has been widely studied in fruit flies, and is one of the reasons the Tasmanian Devil is in such trouble with the facial tumour disease, because there’s just not enough variation in the population at the moment, because they’ve been through too many bottlenecks.

SHANE HUNTINGTON
I guess in that particular case, where something like the Tasmanian Devil is isolated to a particular region, if that is not one of the refuges that we’re talking about, one of these areas that species contract to, what happens to those particular species?  Do they just die out if they can’t adapt?

KATE NAUGHTON
Yeah, if they can’t adapt or migrate to a more favourable environment, where there’s sort of room for them to grow then, yes, they’ll just basically go extinct.

SHANE HUNTINGTON
What sort of characterises these refuges as being places where I guess everything goes to to survive?

KATE NAUGHTON
It depends what sort of environment you’re looking at.  But, for example, if you’re looking at a glacial period and a species prefers slightly warmer temperatures, it’ll be places where that warmer condition will persist.  For example, if you’re looking at the South Australian coastline, it will be slightly further north, they would try and shift in that general direction over generations, depending how fast the change is coming along.

SHANE HUNTINGTON
I understand that these sorts of studies around these refuges, or refugia as you call them, have been done quite extensively in terrestrial systems?

KATE NAUGHTON
Yeah.

SHANE HUNTINGTON
So on land?

KATE NAUGHTON
Yeah.  So there’s been quite a lot of work done particularly in Europe, and also in North America, studying various mammalian species, hedgehog, bear, that sort of thing, and also a lot of trees.  There’s a really good pollen fossil record, so it’s quite - well, I won’t say easy, but there’s a lot of resources to be able to track the expansion fronts and retreats in response to climate change.  It also relates a lot to population connectivity.  So, for example, how connected different populations are, as to how well this migration can happen.

SHANE HUNTINGTON
Now, Kate, you work specifically on the southern Australian coastline.  Our international listeners will know where Sydney and Melbourne and even the Great Barrier Reef are.  Whereabouts are you looking specifically along that coastline for your genetic specimens?

KATE NAUGHTON
Well I’m actually looking at Byron Bay, which is on the east coast, and Fremantle on the south - sort of on the southern side of the west coast of Australia, and around Tasmania.  So that’s a coastline of about 8000 kilometres.  It’s a fairly extensive coastline.  But the reason I’ve chosen those endpoints is they are actually the endpoints of many reported species distributions, so they represent sort of turnover sites between tropical and temperate species.

SHANE HUNTINGTON
And this is I guess the entire bottom half of Australia essentially you’re looking at in many regards.  You’ve chosen the echinoderms, which are things like starfish.  Why have you chosen these particular creatures to study?

KATE NAUGHTON
There’s a few reasons.  Again there’s an emotional reason, that I just like them, because they’re a bit weird.  But also they’re a really interesting set of species to study because they’re quite diverse in terms of their life history.  For example, there are some that brood their young, there are some that spawn freely, and those sort of patterns show different levels of population connectivity.  So if I’m doing a comparative project across a number of species, I can look at species that reproduce in different ways and see how this affects their distribution, their connectivity, their levels of genetic diversity, and if that affects where these refugia might be located.

SHANE HUNTINGTON
So tell us a little bit about starfish.  How do they reproduce?  This is something I have to say, thinking about it now, I have no idea.  Are they producing vast quantities of offspring?

KATE NAUGHTON
Some of them are.  It’s extremely variable.  For example, there’s a very small species that’s largely restricted to Tasmania, that produces live young, and it can only produce a few because it broods them inside the gonad, it’s a self-fertilising hermaphrodite, and they burst out of the parent because they’re not really built for giving birth as such.  But then there are species which produce thousands and thousands of larvae per individual, and they’re amazingly fecund species.  So there’s an enormous array of diversity within the starfish and within the echinoderms in general, in terms of reproduction.

SHANE HUNTINGTON
Kate, with regards to the movement of these particular creatures, are they very rapid-moving?  You obviously didn’t choose fish as the example you’re looking at, you’re using starfish.  How sort of mobile are they?

KATE NAUGHTON
Well individuals don’t move very far as a general rule.  You can pretty much flip them on their backs, go away for five minutes and you’ll come back and they may have flipped over if you’re lucky.  But the larvae are really the life-history phase that dictates how far these animals can migrate or move, and obviously that’s between generations. It depends on what kind of larvae a starfish will produce.  

For example, there are some that can produce feeding larvae, which travel extraordinarily long distances and can be as long as a three-month, six-month larval phase, although that’s extreme.  Or there’s another species that I’m working on, which is the Little Biscuit Star, and there’s one particular type of Biscuit Star that produces brooded larvae that don’t swim, they can’t swim at all, they don’t have cilia, which are the little hairs that allow larvae to swim.  They are only in their larval form for about three days, and much of that is a form that actually attaches to nearby surfaces, so they don’t swim.  So they obviously can’t get about very well.

SHANE HUNTINGTON
When you’re out there you’re looking at the genetics of these particular life forms, what do you hope to learn from the genetics in terms of these various species?

KATE NAUGHTON
What I hope to learn is essentially where areas of high diversity within species, so intra-specific genetic diversity, are located.  For example, are they more diverse on the sort of northern edge of the west coast - well the northern edge of the area I’m looking at - are they more diverse in the South Australian, or around the southern point of Tasmania, where a coldwater species might perhaps persist over long periods of time.

To give you an example, Melbourne sits on Port Philip Bay, and it’s very shallow.  At its deepest point it gets down to about 30 metres, but most of Port Philip Bay is about 10 metres deep.  So that actually - due to sea level change that actually disappears during glacial periods, so any species that is currently located in Port Philip Bay, any non-migratory species, will have been there for less than say about 10,000 years.  And because of that, they tend to have a much lower level of genetic diversity.  They haven’t persisted in the same place for as long a time, so the population will be dominated by the sort of genetic signature, I guess you’d call it, of the founding individuals of that population.  Now that’s called a founder effect, and that tends to characterise a population that is recently expanded or recently founded.

SHANE HUNTINGTON
So this means that when you look at the genetic studies of these particular animals and so forth, and I guess you could do it with plants and various other things as well, you’re able to determine what the climatic conditions have been, in some sense, or what the major shifts have been, over a long period, and whether or not, relative to that genetic diversity, this area is one of these refuges taken up in the last sort of major climate shift?

KATE NAUGHTON
Well in terms of the conditions at the time I sort of stand on the shoulders of giants and go and look at geological paleo-ecological data so that I can try and work out what the conditions were, what the sea level would have been around that time, and then I try and correlate that data with the genetic data that I’m getting.  And what I expect to find, according to my hypothesis, is that these areas of high intra-specific, sort of within species, genetic diversity will correlate with more favourable conditions during glacial periods.  Or, conversely, during inter-glacial periods for species that might prefer cold water, because I do have one species that sort of fulfils those criteria.

SHANE HUNTINGTON
So in your initial studies, looking around Australia, are there areas where you sort of can predict, based on this genetic material, that this will be a high-risk area, as a result of low genetic diversity that you find there?

KATE NAUGHTON
Yes, you can actually predict that fairly well just by looking at the genetic diversity within a species.  You can predict that.  It’s fairly - it’s what we call monomorphic, there’s not a lot of variation in there.  That tends to mean that it’s not a persistent population, it’s been established recently, it’s not stable as such over really long periods of time, and it also means that they’re less adaptable to change, there’s less room in the genome, so to speak, for favourable mutations to result in better survival...

SHANE HUNTINGTON
Advantages.

KATE NAUGHTON
Yeah, advantage.

SHANE HUNTINGTON
And, Kate, when you - so when you look at the outcomes from trying to find this link between the genetic diversity and the locale that you find them in, how will that enable us to sort of better prepare for mitigation of species risk down the track?

KATE NAUGHTON
Well, it’s really good in a particular sense, because what we’re identifying through this is source and sink populations.  Sink populations being those that repeatedly need to be re-established over time, and source populations obviously being those which persist for longer.  If you identify your source population and you can protect that source population well, for example if you have a marine national park or sanctuary at that site, then you’re doing a really good thing, not only for that ecosystem but for the surrounding ecosystems if they need to recover from damage, storm damage, climate change, pollution, whatever.  If they need to recover, you’ve got your source population there to help recolonise your damaged habitat.

SHANE HUNTINGTON
So it seems as though we could definitely do well by augmenting our efforts into areas where there is potentially a much more large diversity of genetic material and groups, and perhaps some of the ones where it’s limited, even though they may look like ones we want to save, if we have to pick our battles we may be better to leave them alone.

KATE NAUGHTON
Well basically if you’re choosing between habitat with high genetic diversity and lower, obviously you would go with the higher genetic diversity because that’s what you really want to preserve, because these sites act as an archive really for that species.

SHANE HUNTINGTON
Kate, we wish you the very best of luck with your research endeavour, and we thank you very much for being our guest today on Up Close.

KATE NAUGHTON
Thank you very much.

SHANE HUNTINGTON
Our second PhD student in this episode is Miss Felicity Jackling, also from the Department of Genetics at the University of Melbourne, Australia.  Felicity is studying a range of genetic disorders that occur in populations of alpacas.  Alpaca herds are farmed in many countries around the world.  Addressing questions relating to genetic disorders may lead to long-term improvements for domesticated livestock.  Welcome to Up Close, Felicity.

FELICITY JACKLING
Thank you very much for having me.

SHANE HUNTINGTON
First of all, can you describe for us the alpaca.  Some people know what it is, but what’s it related to closely?

FELICITY JACKLING
Okay, well it is very similar to a llama, that is the species that it’s most closely related to.  They are about human height, ranging about five to six feet, they can be up to about 60 to 70 kilos, and they’re quite cute and cuddly animals, and they make quite good pets actually.

SHANE HUNTINGTON
Whereabouts in the world do the majority of the alpaca populations live?

FELICITY JACKLING
The alpaca has been domesticated from a species called the vicuna, over in South America, and the main alpaca population is over in South America, although we do have Australian alpacas, and there’s also herds in New Zealand and the US.

SHANE HUNTINGTON
You mentioned the word herds. Are they in large groups, or do they head off individually?  How do they sort of cooperate with each other in the wild?

FELICITY JACKLING
In the wild they’re normally found as herds, and in the domesticated species in Australia we have about 80 per cent of herds are less than 10 animals, whereas there are some quite large herds with say over 2000 animals. So it can range quite a bit.

SHANE HUNTINGTON
What’s the main purpose for us breeding alpacas in a domesticated sense?

FELICITY JACKLING
Alpacas have an amazing fleece, both in quantity and quality.  The alpaca fleece is quite amazing.  To go up and touch and feel alpaca fleece is quite an experience in itself, and that fleece is very much sought after.  And I should point out that there are two fleece types in alpacas, which are very distinct.  One is the huacaya fleece type, which is more similar to a sheep fleece and is very fluffy.  The other type of fleece is called the suri fleece, and the suri fleece is worth more than a huacaya fleece.  The suri fleece actually looks a little bit like dreadlocks and hangs from the animal quite low to the ground, and curls in long locks.

SHANE HUNTINGTON
When you look at many other animal species you find that they have been evolved over a long period of time for specific purposes.  Is that the case in the alpaca?  Do these two fleece types serve a specific purpose in terms of their survival, or have we sort of bred them that way?

FELICITY JACKLING
Well occurring in the wild, the suri and huacaya fleeces both exist.  The suri fleece is much rarer though.  Over in South America only about five per cent of alpacas have the suri fleece.  A cost to having the suri fleece is that because the fleece kind of  joins together and forms a lock, on the back of the animal the locks can part and some of the skin is exposed to the cold climate.  So that can act as a deficit for an animal, so we think that evolution has acted to reduce the percentage of animals with the suri fleece type.

Now in a domesticated sense, and especially for breeding alpacas, we would like a higher percentage of suri animals.  So compared to the world prevalence of suri fleece types, of five per cent, in Australia we have 10 per cent that are suri.

SHANE HUNTINGTON
Are there other attributes in the alpacas that we specifically breed towards a certain standard or a certain body type, or other attribute that might be important?

FELICITY JACKLING
Yes, absolutely.  Breeders are very interested in going down to the fine characteristics of fleece type.  So even though you’ve got this major difference in fleece type between the suri and huacaya, we’re now going down to looking at the thickness and thinness of individual hairs.  Also the lustre or how shiny the hair looks is really important.  Breeders are really interested in having a uniformity of fleece quality over the body of the animal so that they can use all the fleece from the animal.

SHANE HUNTINGTON
When you breed so specifically for something like fleece, do you find that because of the sort of genetic interactions within the species that there are similarities in other phenotype aspects of the alpaca as well?  I mean do they all end up being the same height or the same length, or are they decoupled from the fleece-breeding aspects?

FELICITY JACKLING
There are certainly characteristics that seem to be inherited together.  There’s quite a kind of strange phenomenon where I’ve spoken to some breeders and they’ve said, look, we’ve had some really, really sickly animals with some horrible genetic defects, but their fleece is the best we’ve ever seen.  So it seems that the good fleece characteristics can be inherited alongside some genetic defects.  So it’s true that some characteristics can be inherited together, whereas others can be quite separate.

SHANE HUNTINGTON
Felicity, going on from the breeding for specific fleece types, I can imagine there would be a number of congenital disorders that end up in the population as a result of that, just as we see in the canine breeding programs around the world.  

FELICITY JACKLING
Yes.

SHANE HUNTINGTON
Can you speak to that?

FELICITY JACKLING
Yes, absolutely.  There generally is a low prevalence of genetic defects in any livestock population, but what we’re seeing in alpacas is that due to this very selective breeding we’ve seen a reduction in genetic diversity within alpacas, and that’s really led to an increase in the prevalence of genetic disorders.  In fact a veterinarian associated with our project has told us that she’s seen more genetic defects in alpacas than all other livestock combined.  

So it’s really becoming a serious problem in alpacas, and that’s what our research really is trying to aim at, understanding the genetic basis of some of these disorders, and also trying to educate breeders that mating animals that are closely related can give you these defects.  And it’s quite unfortunate that some of the current veterinary advice is that if a breeder does have an alpaca born with a genetic defect, they’re told to just avoid that particular mating with those two individuals again.  However, some of these disorders are recessive in nature, which means that even an unaffected animal can produce offspring with a genetic defect.  So that current veterinary advice is really only acting to perpetuate the inheritance of some of these disorders.

SHANE HUNTINGTON
In addition to this relatively poor veterinary advice, I assume the only way to deal with this currently is to euthanase the animals in question?  Is that the response?

FELICITY JACKLING
Some of the genetic defects are so severe that they affect the health, to the point of they would either die naturally very young, some of them are euthanased for humane reasons, whereas others are kept out in a back paddock somewhere.  A kind of embryo transfer program has been developed in alpacas, and so they can be used as recipient females for breeding purposes.

SHANE HUNTINGTON
You’re working on the genetics of this problem.  Do we know what the actual genetic causes are of the conditions that you’re talking about, that we’re finding in these closely-bred alpacas?

FELICITY JACKLING
Some of these conditions are very poorly studied, and not very much is known about them at all.  Some of the conditions, however, do occur in humans or other well-studied organisms, and in those cases we do have an idea of possibly some of the genes that cause these defects in humans are the same ones causing the defects in alpacas.  So they’re what we would call good candidate genes that we would be really interested in following up in alpacas.

SHANE HUNTINGTON
Felicity, can you give us an example of some of the sort of defects that we would see in the alpaca population?  You mentioned in some cases they cause death, but I assume there’s a whole spectrum of possible outcomes.

FELICITY JACKLING
Absolutely.  There are two common facial defects in alpacas.  One is called wry face, which is essentially a twisted jaw, and that can actually be really quite severe, affecting the ability of the animal to eat, you know, a substantial amount of food, or amount of food to keep it alive.  The other common defect is called choanal atresia, and all that really means is that the nasal passages of the animal don’t form properly, and so it has a lot of trouble breathing through its nose.  Now in adulthood they can simply open their mouths and breathe through their mouths, but it does become a problem when they’re feeding as young, and milk can enter the lungs and cause pneumonia.  

So they’re kind of two examples where death can occur.  We do have other defects such as polydactyly, which is just extra toes.  So those animals their kind of life expectancy isn’t severely affected by that kind of disorder.

SHANE HUNTINGTON
How do we go about isolating the specific genes that are responsible for these problems?

FELICITY JACKLING
In terms of a genetic mapping process, we’re really interested in going down to the fine detail of what particular genes are causing these disorders.  And what we really need for that is as many samples as we can get, from animals that are affected with disorders.  But also what is really helpful in the mapping process is to have relatives of affected individuals, and it doesn’t matter if they’re affected or unaffected, but they will help in the mapping process.  

And so in simple terms the way we go about it is looking for a difference in the genetics between affected and unaffected individuals that can account for the difference in the disease that we see.

SHANE HUNTINGTON
And then I assume you also have to pull out those that are recessive, that aren’t actually sort of showing a particular problem but have the genetic flaws inherent in the affected population?

FELICITY JACKLING
That’s right.  So we can - once we can identify the gene we can then go back through a pedigree and deduce that that individual is actually carrying the defective gene and has passed it on to a number of relatives or offspring.

SHANE HUNTINGTON
Felicity, we wish you the very best of luck with your research endeavour, and thank you very much for being our guest on Up Close today.

FELICITY JACKLING
Thank you very much for having me.

SHANE HUNTINGTON
Relevant links, the full transcript, and more info on this episode can be found at our website, at upclose.unimelb.edu.au.  We also invite you to leave your comments or feedback on this or any episode of Up Close.  Simply click on the ‘add new comment’ link at the bottom of the episode page.

Melbourne University Up Close is brought to you by Marketing and Communications of the University of Melbourne, Australia.  Our producers for this episode were Kelvin Param and Eric van Bemmel.  Audio engineering by Russell Evans.  Theme music by Sergio Ercole.  Melbourne University Up Close is created by Eric van Bemmel and Kelvin Param.  I’m Dr Shane Huntington.  Until next time, goodbye.

VOICEOVER
You have been listening to Up Close.  For more information visit upclose.unimelb.edu.au.  Copyright 2010, The University of Melbourne.


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